[gmx-users] Disulphide bonded cyclic peptides

Tue Dec 3 12:51:52 CET 2019

Hello, 

In the entries of the forcefied file *.rtp, *n.tdb and in *c.tdb. 

Yes I figured eventually that it was a stupid question to ask :) 

Thank you so much. 

On 2019-12-03 13:44, Alessandra Villa wrote:

> Hi
> 
> On Sat, Nov 30, 2019 at 2:04 PM Sahil Lall <slall at ncbs.res.in> wrote:
> 
> Thank you Alessandra.
> 
> I am extremely grateful for your help. It worked!
> 
> However, one last bit
> 
> You suggested to
> 
> use the one of the backbone
> for your new entry (since you do not have a real termini) for CYS-1
> N    opls_238   -0.500     0
> H    opls_241    0.300     0
> CA    opls_224B   0.140     1
> 
> You could also directly change the charges in the top file. 
> Apart from the top file, where could have I specified the opls_X
> atomtypes?
 In the entries of the forcefied file *.rtp, *n.tdb and in *c.tdb.
Best regards
Alessandra

> Best regards,
> 
> Sahil
> 
> On 2019-11-29 15:46, Alessandra Villa wrote:
> 
>> Hi,
>> 
>> On Fri, Nov 29, 2019 at 8:30 AM Sahil Lall <slall at ncbs.res.in> wrote:
>> 
>> Hello,
>> 
>> Thank you for your suggestions, gave me some insight into my own work.
>> However, the problem still persists.
>> 
>> With the option -ignh, you request pdb2gmx to add H atom. Thus, if you
> have  already H atoms in the pdb I suggest to remove the option -ignh. 
> 
>> I had already tried removing the -ignh option before posting this here
>> but did not find success.
>> 
>> Did you try also without -ter?
>> 
>> Removing the -ter option does not work in any combination. It always
>> overrides everything else and breaks the cyclising peptide bond into
>> NH3+ and COO-.
>> 
>> .
>> 
>> Another option could be to remove the extra H from gro/pdb file you got
> from pdb2gmx, remove H, (if you want, fix the atom number using editconf), 
> 
>> then try to use the so obtained pdb/gro file as input to pdb2gmx (without
>> -ter -ignh)
>> 
>> So this also does not work. pdb2gmx breaks the peptide bond without the
>> -ter option.
>> 
>> I tried putting a new entry in the OPLS aminoacids.n.tdb file as you
>> suggested. I used the opls_910 planar hydrogen for secondary amines as
>> shown below
>> 
>> [ CYS2-NH ]
>> [ replace ]
>> N opls_900 14.0027 -0.9
>> CA opls_912B 12.011 0.12
>> [ add ]
>> 1 1 H N CA C
>> opls_910 1.008 0.36
>> [ delete ]
>> H
> You got a charged system, probably because you have generated a new
> entry
> without accounting for the partial charge.
> 
> As atomic charge and atom types I suggest to use the one of the backbone
> for your new entry (since you do not have a real termini) for CYS-1
> N    opls_238   -0.500     0
> H    opls_241    0.300     0
> CA    opls_224B   0.140     1
> 
> You could also directly change the charges in the top file.
> 
> I hope this solve the problem
> Best regards
> Alessandra
> 
> Now I can get the peptide bond correctly but the system is charged.
> 
> Output below:
> 
> Identified residue CYS1 as a starting terminus.
> Identified residue CYS6 as a ending terminus.
> 2 out of 2 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> CYS1 CYS1 CYS1 CYS6 CYS6
> N1 C3 SG6 N87 C89
> CYS1 C3 0.244
> CYS1 SG6 0.312 0.419
> CYS6 N87 0.335 0.510 0.486
> CYS6 C89 0.136 0.373 0.322 0.239
> CYS6 SG92 0.387 0.482 0.205 0.420 0.365
> Linking CYS-1 N-1 and CYS-6 C-89...
> Linking CYS-1 SG-6 and CYS-6 SG-92...
> Select start terminus type for CYS-1
> 0: CYS2-NH
> 1: NH3+
> 2: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
> residue)
> 3: NH2
> 4: None
> 0
> Start terminus CYS-1: CYS2-NH
> Select end terminus type for CYS-6
> 0: COO-
> 1: ZWITTERION_COO- (only use with zwitterions containing exactly one
> residue)
> 2: COOH
> 3: None
> 3
> End terminus CYS-6: None
> Checking for duplicate atoms....
> Generating any missing hydrogen atoms and/or adding termini.
> Now there are 6 residues with 96 atoms
> Making bonds...
> Number of bonds was 99, now 98
> Generating angles, dihedrals and pairs...
> Before cleaning: 258 pairs
> Before cleaning: 258 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...There are 258 dihedrals, 21 impropers, 174 angles
> 255 pairs, 98 bonds and 0 virtual sites
> Total mass 734.892 a.m.u.
> Total charge -0.420 e
> Writing topology
> 
> Any ideas?
> 
> Extremely thankful
> 
> Sahil
> 
> On 2019-11-28 20:15, Alessandra Villa wrote:
> 
> Hi again,
> 
> On Thu, Nov 28, 2019 at 11:06 AM Sahil Lall <slall at ncbs.res.in> wrote:
> 
> Hello,
> 
> I am extremely thankful for your suggestions, but I have a few concerns
> with your advice as stated below.
> 
> Hi,
> Below some suggestion that may help you.
> 
> On Wed, Nov 27, 2019 at 7:44 AM Sahil Lall <slall at ncbs.res.in> wrote:
> 
> Dear community,
> 
> I want to use the OPLS-AA ff to understand the dynamics of a cyclic
> peptide with terminal Cystines that are disulphide linked. To cyclise
> the N- and C- termini, I used a special bond in a specbond.dat file
> placed in my working directory.
> 
> 2
> CYS N 1 CYS C 1 0.14 CYS CYS
> CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
> 
> and after the pdb2gmx command I get the following response
> 
> Identified residue CYS2 as a starting terminus.
> Identified residue CYS7 as a ending terminus.
> 2 out of 2 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> CYS2    CYS2    CYS2    CYS7    CYS7
> N1      C3     SG6     N45     C47
> CYS2      C3   0.244
> CYS2     SG6   0.312   0.419
> CYS7     N45   0.335   0.510   0.486
> CYS7     C47   0.136   0.373   0.322   0.239
> CYS7    SG50   0.387   0.482   0.205   0.420   0.365
> Linking CYS-2 N-1 and CYS-7 C-47...
> Linking CYS-2 SG-6 and CYS-7 SG-50...
> 
> However, the problem arises with the -ter flag in the pdb2gmx command
> 
> pdb2gmx -f in.pdb -o out.gro -ter -ignh
> 
> With the option -ignh, you request pdb2gmx to add H atom. Thus, if you have  already H atoms in the pdb I suggest to remove the option -ignh.
> 
> I had already tried removing the -ignh option before posting this here
> but did not find success.
> 
> Did you try also without -ter?
> 
> In alternative,  you could try add a new entry in the file opls force
 field 

> file aminoacids.n.tdb for your CYS termini (e.i in place of NH2 put NH).
 In 

> alternative you can use the file that you got using NH2 as N-terminus,
 and 

> manually remove the extra H you  have connected to N (both from top and
 gro 

> file). This operation requires to be very careful since you have to
 remove 

> the correct H.
> If I remove the extra hydrogen after getting the pdb2gmx output, will I
> not have to edit the topology file also?

Yes you should fix also the top file, including  removing all the
interactions that involve the removed H

Another option could be to remove the extra H from gro/pdb file you got
from pdb2gmx, remove H, (if you want, fix the atom number using
editconf),
then try to use the so obtained pdb/gro file as input to pdb2gmx
(without
-ter -ignh)

> And will changing the CYS
> termini in the force field .tdb file not mess with anything else as far
> as the force field parameters are concerned?
   If properly done, no

Best regards
Alessandra

> Thankful,
> 
> Sahil
> 
> Best regards
> Alessandra
> 
> The output is fine and links the terminal Cystines and putting a
   disulphide bond between them as shown above. But doesn't seem to be

>> happy with the -ter command.
>> 
>> Select start terminus type for CYS-2
>> 0: NH3+
>> 1: ZWITTERION_NH3+ (only use with zwitterions containing exactly one
>> residue)
>> 2: NH2
>> 3: None
>> 3
>> Start terminus CYS-2: None
>> Select end terminus type for CYS-7
>> 0: COO-
>> 1: ZWITTERION_COO- (only use with zwitterions containing exactly one
>> residue)
>> 2: COOH
>> 3: None
>> 3
>> End terminus CYS-7: None
>> 
>> -------------------------------------------------------
>> Program pdb2gmx, VERSION 4.6.7
>> Source code file:
>> /home/ncbs/Downloads/gromacs-4.6.7/src/kernel/pdb2top.c, line: 1109
>> 
>> Fatal error:
>> There is a dangling bond at at least one of the terminal ends. Fix your
>> coordinate file, add a new terminal database entry (.tdb), or select the
>> proper existing terminal entry.
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> 
>> I cannot understand what is going wrong. The command only works if I
>> choose NH2 as my N-terminus, however that in principle violates the
>> neutrality of the system.
> 
>> Thanks,
>> 
>> Sahil
>> --
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